Contacts of the strand formed by residues 153 - 158 (chain G) in PDB entry 1VYH
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 153 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112G THR* 3.0 25.5 + - - -
126G ALA* 3.7 22.4 - - + +
127G SER 2.9 18.9 + - - +
130G ALA* 3.7 23.1 - - + -
131G THR 3.7 10.3 - - - +
132G ILE* 4.1 5.8 - - + -
149G HIS* 3.7 18.2 - - + -
152G SER* 1.3 76.5 - - - +
154G GLN* 1.3 59.5 + - - +
155G ASP 3.8 12.3 - - - +
167G SER* 4.0 16.2 - - - -
168G CYS 3.0 12.3 - - - +
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Residues in contact with GLN 154 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E ASP* 5.7 3.2 - - - +
112G THR* 3.5 21.3 - - + +
113G ARG* 2.9 32.5 + - - +
126G ALA* 5.2 0.4 - - - -
128G GLU* 4.5 9.7 + - - -
152G SER* 3.6 26.4 + - - -
153G VAL* 1.3 74.5 - - - +
155G ASP* 1.3 58.3 + - - +
168G CYS 2.7 10.7 + - - -
170G ALA* 3.7 12.4 + - - +
194G ASN* 2.7 38.3 - - - +
195G VAL 3.5 16.8 - - - +
196G SER* 4.0 15.5 - - - +
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Residues in contact with ASP 155 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G ARG* 2.6 45.9 + - - +
153G VAL* 3.8 4.4 - - - +
154G GLN* 1.3 76.3 - - - +
156G ILE* 1.3 78.3 + - - +
167G SER* 3.4 3.5 - - - -
168G CYS* 3.1 31.0 + - - +
196G SER 4.2 0.2 - - - +
197G SER* 3.7 11.7 - - - -
198G VAL* 2.9 45.3 + - - +
241G ARG* 3.2 17.9 + - - -
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Residues in contact with ILE 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G ARG* 3.7 22.3 - - + +
114G VAL 4.7 0.4 - - - +
115G ILE* 3.0 29.3 - - + +
124G VAL* 4.3 17.7 - - + +
125G SER* 3.8 7.9 - - - -
126G ALA* 3.2 42.4 - - + +
132G ILE* 5.1 4.7 - - + -
153G VAL* 4.9 1.8 - - + -
155G ASP* 1.3 93.3 + - - +
157G SER* 1.3 62.2 + - - +
165G LEU* 3.1 35.0 - - + -
166G ALA 3.4 7.6 - - - +
167G SER* 5.5 1.6 - - - -
198G VAL* 4.4 2.5 - - - -
241G ARG* 5.3 1.2 + - - -
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Residues in contact with SER 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115G ILE* 4.0 5.8 - - - -
156G ILE* 1.3 79.0 - - - +
158G PHE* 1.3 65.3 + - - +
165G LEU* 3.9 4.3 - - - -
166G ALA* 3.0 31.6 + - - -
198G VAL* 3.6 22.9 - - - -
199G SER* 3.4 8.0 - - - -
200G ILE* 2.9 35.5 + - - +
241G ARG* 5.5 2.2 - - - -
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Residues in contact with PHE 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115G ILE* 4.0 20.6 - - + +
116G PHE 3.5 10.8 - - - +
117G HIS* 3.4 42.8 - + + -
118G PRO* 3.5 26.0 - - + -
124G VAL* 3.7 15.5 - - + -
157G SER* 1.3 83.6 + - - +
159G ASP* 1.3 69.0 + - - +
162G GLY* 4.7 5.8 - - - -
164G LEU 3.5 12.3 - - - -
165G LEU* 3.5 30.7 - - + +
179G PHE* 3.6 26.5 - + - -
200G ILE* 3.8 7.3 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il